TABLE OF CONTENTS

1. Overview 8
1.1 Statement of Report 8
1.2 About this Report 8
1.3 Scope of this Report 10
1.4 Methodology 10
1.5 Executive Summary 11

2. Introduction 13
2.1 Global Bioinformatics Products Industry 14
2.2 Computers and Biology 15
2.3 Bioinformatics and the Internet 17
2.4 Company Evaluation Overview 17
2.5 Market Outlook 18
2.6 Competitive Structure 20
2.7 Applications of Bioinformatics 20
2.7.1 Medicine 20
2.7.2 Microbial Genomics 22
2.7.3 Agriculture 22
2.8 R&D 22
2.8.1 Allocation of R&D 23
2.8.2 Traditional Drug Discovery Process 24
2.8.3 Drug Discovery and Bioinformatics 26
2.8.4 Collaborative Agreements 27
2.9 The Human Genome Project (HGP) 27
2.9.1 Goals of the Human Genome Project 27
2.9.2 Benefits of the Human Genome Project 29
2.10 Barriers to Entry 29
2.11 Proteomics and Databases 30
2.11.1 Protein Database Standards 31
2.11.2 Future Trends 32

3. The U.S. Bioinformatics Market 33
3.1 Overview 33
3.2 Market Restraints and Drivers 35
3.2.1 Market Restraints 35
3.2.2 Market Drivers 36

4. Genomics 37
4.1 The Biotechnology Industry 37
4.2 The Development of a Genomics Market 39
4.2.1 Market Drivers 40
4.2.2 Market Restraints 40
4.2.3 Market Size and Growth Projections 40
4.2.4 The U.S. Genomics Market 40
4.3 Biochips and DNA Microarrays 40
4.3.1 Key Challenges 42
4.3.2 Freeware 42
4.3.3 New Tools 43
4.4 Bioinformatics 46
4.5 Disease Targets 46
4.6 Functional Genomics 47
4.7 Gene Sequencing 50
4.8 Gene Sequence Variation Detection 50
4.9 Comparative Genomics 51
4.10 Genome Database Arrays 51
4.11 High-throughput Genomics 53
4.11.1 High-throughput Technology 54
4.11.2 Lab on a Chip 54
4.12 Pharmacogenomics 55
4.13 Probe Arrays 57
4.13.1 Gene Expression Monitoring Arrays 57
4.13.2 DNA Analysis Arrays 59
4.14 Proteomics 60
4.15 Sequencing 61
4.16 Single Nucleotide Polymorphisms (SNPs) 61
4.17 Structural Genomics 63
4.18 Photolithography 63
4.19 Instrumentation 64

5. The Bioinformatics Industry 65
5.1 Definition and Role of Bioinformatics 65
5.1.1 Bioinformatics Sector Overview 66
5.1.2 The Future Status of Bioinformatics 67
5.1.3 Barriers to Growth 67
5.2 Types of Data and Bioinformatics Applications 67
5.2.1 Validated Core Modeling Technology 68
5.2.2 Broad Applicability 69
5.2.3 Data Management Compliant with Industry Standards 69
5.2.4 Open Architecture 69
5.2.5 Ease of Use 69
5.2.6 Increased Access 69
5.3 Functions of Bioinformatics Software 70
5.3.1 Data Management 70
5.3.2 Data Transformation 70
5.3.3 Data Collaboration 70
5.3.4 Interface for Online Data Sources 70
5.4 Target Markets for Informatics Software 71
5.5 Steps Involved in Bringing a Drug to Market 71
5.6 Costs Incurred in Developing a New Drug 72
5.7 Industry Drivers and Challenges 72
5.8 Industry Risks 74
5.9 Products of Bioinformatics 75
5.10 Bioinformatics Processes 76
5.11 Informatics Tools and Functionalities 76
5.11.1 Sequence to Structure 76
5.11.2 Lead Identification and Optimization 77
5.11.3 Development and Formulation 77
5.11.4 Improving Materials and Processes 77
5.11.5 Other Materials-Based Industries 78
5.12 Role of Bioinformatics in the Biotechnology Value Chain 78
5.13 Bioinformatics Market Segment 78
5.13.1 Databases 78
5.13.2 Hardware 80
5.13.3 Software 80
5.13.4 Bioinformatics Services 81
5.14 Bioinformatics Market Size 82
5.14.1 Sales and R&D 82
5.14.2 IT Budget 83
5.14.3 Projected Bioinformatics Market Size 84
5.15 Global Market Perspective 85

6. Bioinformatics Business 88
6.1 Bioinformatics Business Models 88
6.1.1 Changing Business Models 89
6.1.2 Competition for Pure Play Informatics Companies 91
6.1.3 Non-Profit Organizations 91
6.1.4 In-House Bioinformatics Solutions 91
6.1.5 Large IT Companies 91
6.2 Bioinformatics Target Disciplines 92
6.2.1 Comparative Genomics 92
6.2.2 Pharmacogenomics 92
6.2.3 Functional Genomics 92
6.2.4 Proteomics 93
6.2.5 Structural Genomics 94
6.2.6 Image Informatics 94
6.2.7 Clinical Trial Informatics 95
6.2.8 Cheminformatics 95
6.3 Bioinformatics Architecture 96
6.4 Bioinformatics Applications 97
6.4.1 Data Search Tools 97
6.4.2 Data Visualization Tools 97
6.4.3 Data Mining and Clustering 98
6.4.4 Enterprise Solutions 99
6.4.5 Data Warehousing 99
6.5 Evaluation of Bioinformatics Solutions 99
6.5.1 Requirements of Study 99
6.5.2 Shortlisting the Options 99
6.5.3 Scoring Patterns 100
6.5.4 Performance 101
6.5.5 Data Storage 101
6.5.6 Data Management in Drug Discovery 102
6.5.7 Key Issues in Bioinformatics Data Storage 102
6.6 Convergence of Industries 103
6.7 Proteins as a Driver 104
6.8 Current Bioinformatics Research 104
6.9 New Bioinformatics Modeling Algorithms 105
6.10 3D Modeling 105
6.11 Patenting Bioinformatics Algorithms 106
7. Recent Industry Activity 109
7.1 Collaborations and Acquisitions 109
7.2 Product Development and Launches 111

8. Corporate Profiles 114
8.1 Abbott Laboratories 114
8.2 Abgenix 114
8.3 Ablynx 115
8.4 Accelrys 115
8.5 Affimed Therapeutics 117
8.6 Affitech 118
8.7 Affymetrix 118
8.8 Agencourt Bioscience Corporation 119
8.9 Agensys 120
8.10 Agilent Technologies 120
8.11 Alexion Pharmaceuticals 121
8.12 AlgoNomics 121
8.13 ALLEZ Software 122
8.14 Amgen 123
8.15 Antisoma 124
8.16 Applied Biosystems 124
8.17 Arana Therapeutics 126
8.18 Ariadne Genomics 127
8.19 Array Genetics 127
8.20 Astellas Pharma 128
8.21 AstraZeneca 128
8.22 Automated Handling Systems 129
8.23 Avesthagen, Limited 130
8.24 Bioalma 130
8.25 BIOBASE Biological Databases 131
8.26 BioCarta 132
8.27 Biodatabases (AMITA Corporation) 132
8.28 BioDiscovery 133
8.29 Biogen Idec 133
8.30 BioInformatics 134
8.31 BioInformatics Services 135
8.32 BioInformatics Solutions 135
8.33 Biomax Informatics 136
8.34 BioServe Technologies 136
8.35 Biosiris 137
8.36 BioSoftSolutions 137
8.37 Biotique Systems 137
8.38 BioInvent International 138
8.39 Biosite Discovery 138
8.40 BioWa 139
8.41 BioWisdom 139
8.42 Bio-Xtal 140
8.43 Boehringer Ingelheim 140
8.44 Cambridge Antibody Technology Group 141
8.45 Capital Genomix 141
8.46 Celera Group 141
8.47 Cellectis 143
8.48 Cellomics 143
8.49 CeuticalSoft 144
8.50 Chemical Computing Group 145
8.51 Cimarron Software 145
8.52 CLONDIAG Chip Technologies 146
8.53 CodonCode Corporation 146
8.54 CompuDrug International 146
8.55 Compugen USA 147
8.56 Corimbia 148
8.57 Crucell 148
8.58 CSIRO Bioinformatics 149
8.59 CuraGen Corporation 149
8.60 CyberGene 151
8.61 Cytogen 151
8.62 Data Unlimited International 151
8.63 deCODE Genetics 151
8.64 Decodon 152
8.65 Deltagen 152
8.66 Digilab 153
8.67 DNA Software 154
8.68 DNAPrint Genomics 154
8.69 DNA Star 155
8.70 DxS 155
8.71 Dyax Corp. 156
8.72 Eisai 157
8.73 Elan Corporation 157
8.74 Electric Genetics Corporation 159
8.75 Elusys Therapeutics 160
8.76 Entagen 160
8.77 Entelos 160
8.78 Enzon Pharmaceuticals 161
8.79 Epigenomics 162
8.80 ePitope Informatics 163
8.81 EraGen Biosciences 163
8.82 European Bioinformatics Institute (EBI) Industry Programme 163
8.83 Evolutionary BioInformatics 164
8.84 Genamics 164
8.85 GeneData 164
8.86 Gene Logic 165
8.87 Genentech 167
8.88 Geneva Bioinformatics (GeneBio) 168
8.89 Genmab 169
8.90 GenOdyssee 170
8.91 Genolyze 170
8.92 Genomatica 171
8.93 GenomeQuest 171
8.94 Genomic Solutions 172
8.95 Genomining 173
8.96 Genovac 173
8.97 Genzyme 173
8.98 Geospiza 175
8.99 GlaxoSmithKline 176
8.100 Glycominds 176
8.101 Health Discovery Corporation 176
8.102 Hitachi Corporate Technology Group 178
8.103 IBM Life Sciences 178
8.104 ImClone Systems 179
8.105 ImmunoGen 180
8.106 Immunomedics 181
8.107 Improved Outcomes Software 183
8.108 INCOGEN 184
8.109 Incyte Corporation 184
8.110 Informagen 185
8.111 Ingenuity Systems 185
8.112 InNexus Biotechnology 186
8.113 Insilicos 186
8.114 Intrexon Corporation 186
8.115 Invitrogen Corporation 187
8.116 IO Informatics 188
8.117 Johnson & Johnson 188
8.118 LabVantage Solutions 190
8.119 Lexigen 190
8.120 Lifespan Biosciences 190
8.121 Lion Bioscience 190
8.122 MathEcology 191
8.123 Matrix Science 191
8.124 Medarex 191
8.125 Medicel 193
8.126 MedImmune 193
8.127 Merus 193
8.128 METabolic Explorer 194
8.129 Metahelix Life Sciences 194
8.130 Metalife 194
8.131 Micromet 195
8.132 Millennium Pharmaceuticals 195
8.133 Molecular Connections 196
8.134 Molecular Networks 196
8.135 Molecularware 196
8.136 MorphoSys 197
8.137 Nexus Genomics 197
8.138 Nonlinear Dynamics 197
8.139 Novartis 198
8.140 Ocimum Biosolutions 199
8.141 OmniViz 200
8.142 Partek 200
8.143 PDL BioPharma 201
8.144 Perlegen Sciences 203
8.145 Philogen 203
8.146 Philotec 204
8.147 Prokaria 204
8.148 Quantiom Bioinformatics 204
8.149 Relevant Software 205
8.150 Roche 205
8.151 Rosetta Inpharmatics 206
8.152 Sanofi-Aventis 207
8.153 SBI Science 209
8.154 Seascape Learning 209
8.155 Seattle Genetics 210
8.156 Scil Proteins 211
8.157 Simulations Plus 211
8.158 Spotfire 212
8.159 Strand Life Sciences 213
8.160 Sun Microsystems 214
8.161 Symphogen 215
8.162 Syngene 215
8.163 Tahoe Informatics 215
8.164 Tanox 215
8.165 3rd Millennium 216
8.166 ThromboGenics 216
8.167 Thomson Reuters 217
8.168 TIB MOLBIOL 217
8.169 Trion Pharma 217
8.170 Tripos 218
8.171 UBI Life Sciences 218
8.172 Viventia Biotech 219
8.173 VizX Labs 219
8.174 Wyeth 220
8.175 Xcellerex 220
8.176 Xencor 221
8.177 Xoma 221
8.178 Xpogen 223


INDEX OF FIGURES

Figure 4.1: Representation of Biotechnology Market, Geographically, 2008 38
Figure 5.1: Informatics Applications along the Drug-Discovery Value Chain 65
Figure 5.2: Functions of Bioinformatics Software in Research 65
Figure 5.3: EMBL Database Growth, 1995-2008 66
Figure 5.4: The Steps Involved in Bringing a Drug to Market 71
Figure 5.5: The Breakdown of Total Costs in New Drug Development, 2007 72
Figure 5.6: The Role of Bioinformatics in the Biotechnology Value Chain 78
Figure 5.7: Worldwide Pharmaceutical Sales and R&D Expenditures, 2000-2013 83
Figure 5.8: Worldwide Growth in IT Budget, 2000-2013 84
Figure 5.9: Worldwide Bioinformatics Market, 2000-2013 85
Figure 6.1: Steps of a Proteomics Experiment 94
Figure 6.2: Bioinformatics Architecture 96


INDEX OF TABLES

Table 2.1: Leading Biotechnology Companies 21
Table 2.2: Total of Domestic U.S. R&D, 2006-2013 24
Table 2.3: Global Biotechnology Market, 2007 24
Table 2.4: SIB Informatics Databases 31
Table 4.1: The U.S. Biotechnology Industry Size and Revenue, 2000-2007 37
Table 4.2: Global Biotechnology Industry Major Segments 39
Table 4.3: Genomics Sector Market Size, 2006-2013 40
Table 4.4: Total Biochip Market, 2007-2013 41
Table 4.5: Selected Competitors in the Biochip Market 41
Table 4.6: Biochip Microarray Products 41
Table 4.7: Bioinformatics Tools 46
Table 4.8: Functional Genomics Companies Building Advanced Integrated Platforms
and Substantial Databases 49
Table 4.9: Companies Using New Genomic Tools 50
Table 4.10: Non-DNA–Based Chip Suppliers 51
Table 4.11: Robotics or “Lab-on-a-Chip” Market Sector 51
Table 4.12: Key High-throughput and Systemic Approaches in Genomic Analysis 53
Table 4.13: Pharmacogenomics Segment Players 56
Table 4.14: The Worldwide Market for Pharmacogenomics, 2006-2013 56
Table 4.15: Competitors in the SNP Genotyping Segment 63
Table 4.16: Scanning and Detection Technology Suppliers 64
Table 5.1: Data Sources and Bioinformatic Investigations 68
Table 5.2: Drivers and Challenges of the Bioinformatics Industry 73
Table 5.3: Bioinformatics Activities, Sub-Activities and Key Players 81
Table 5.4: Bioinformatics Market Size, 2006-2013 86
Table 5.5: Cheminformatics Market Size, 2006-2013 86
Table 5.6: In-silico Informatics Market Size, 2006-2013 86
Table 5.7: Bioinformatics Hardware and Systems Market Size, 2006-2013 87
Table 6.1: Alliances between IT/Telecom and Biotechnology Firms 103
Table 6.2: Types of Intellectual Property Protection for Bioinformatics Tools
108